Tests:
Correctness tests, verified against a set of known-good resource files.

Caveats:
This is the first pass and my first time writing optimized clojure 1.3. I'm sure there are things that can be improved, so any feedback welcome.

Future:
I've included a modified version of the fastest java program in the patch as I've found it useful for comparison
(# time script/run_java alioth.java.mandelbrot 16000)
One thing we don't have is repeatable performance metrics/tests.
One approach would be to have tests that fail whenever the clojure version falls below a certain percentage of the java version.
That's something I'm working on.

Mike,
I did pull down your repo and ran some tests.
This version of k-nucleotide does run faster than the currently submitted version in alioth.
However, we've got a ways to go to catch the faster Java implementations.

I've added a few comments in your repo.
Of note, the (set! unchecked-math true) directive at the top of files allows us to use inc, dec, etc directly without explicitly specifying unchecked-inc, etc.